NM_005476.7(GNE):c.4G>T (p.Glu2Ter) AND multiple conditions

Clinical significance:Pathogenic (Last evaluated: Feb 20, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001386743.1

Allele description [Variation Report for NM_005476.7(GNE):c.4G>T (p.Glu2Ter)]

NM_005476.7(GNE):c.4G>T (p.Glu2Ter)

Gene:
GNE:glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9p13.3
Genomic location:
Preferred name:
NM_005476.7(GNE):c.4G>T (p.Glu2Ter)
HGVS:
  • NC_000009.12:g.36249352C>A
  • NG_008246.1:g.32693G>T
  • NM_001128227.3:c.97G>T
  • NM_001190383.3:c.4G>T
  • NM_001190384.3:c.-13-2870G>T
  • NM_001190388.2:c.-13-2870G>T
  • NM_001374797.1:c.4G>T
  • NM_001374798.1:c.-13-2870G>T
  • NM_005476.7:c.4G>TMANE SELECT
  • NP_001121699.1:p.Glu33Ter
  • NP_001177312.1:p.Glu2Ter
  • NP_001361726.1:p.Glu2Ter
  • NP_005467.1:p.Glu2Ter
  • LRG_1197t1:c.97G>T
  • LRG_1197t2:c.4G>T
  • LRG_1197:g.32693G>T
  • LRG_1197p1:p.Glu33Ter
  • LRG_1197p2:p.Glu2Ter
  • NC_000009.11:g.36249349C>A
  • NM_001128227.2:c.97G>T
Protein change:
E2*
Links:
dbSNP: rs886044514
NCBI 1000 Genomes Browser:
rs886044514
Molecular consequence:
  • NM_001190384.3:c.-13-2870G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001190388.2:c.-13-2870G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001374798.1:c.-13-2870G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001128227.3:c.97G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001190383.3:c.4G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001374797.1:c.4G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_005476.7:c.4G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
GNE myopathy (NM)
Synonyms:
Nonaka myopathy; Nonaka distal myopathy; INCLUSION BODY MYOPATHY, HEREDITARY, AUTOSOMAL RECESSIVE; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0011603; MedGen: C1853926; Orphanet: 602; OMIM: 605820
Name:
Sialuria
Synonyms:
Sialic Acid Storage Disease; Sialuria, French type
Identifiers:
MONDO: MONDO:0010028; MedGen: C0342853; Orphanet: 3166; OMIM: 269921

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001587091Invitaecriteria provided, single submitter
Pathogenic
(Feb 20, 2020)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Mutation profile of the GNE gene in Japanese patients with distal myopathy with rimmed vacuoles (GNE myopathy).

Cho A, Hayashi YK, Monma K, Oya Y, Noguchi S, Nonaka I, Nishino I.

J Neurol Neurosurg Psychiatry. 2014 Aug;85(8):914-7. doi: 10.1136/jnnp-2013-305587. Epub 2013 Sep 11.

PubMed [citation]
PMID:
24027297

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001587091.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change creates a premature translational stop signal (p.Glu33*) in the GNE gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with GNE-related conditions. ClinVar contains an entry for this variant (Variation ID: 290631). Loss-of-function variants in GNE are known to be pathogenic (PMID: 24027297). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Aug 27, 2021

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